The medium-rare biosphere

All the roots hang down
Swing from town to town
They are marching around
Down under your boots
All the trucks unload
Beyond the gopher holes
There’s a world going on
Underground

— Tom Waits, “Underground”

Our picture of the microbial biosphere is heavily skewed towards what we can see, culture, and are interested in. E. coli is the most touted example: a relatively rare and ineffective bug in our gut became the all-time favorite model organism, because it grows so well in a petri dish, and is easy to manipulate. Our interest in human, animal and crop pathogens is higher than our interest in bacteria that are invovled “only” in nutrient recycling, and both are studied more than those that serve no apparent function, good or bad, in our anthropocentric world.

“One percent!” is the mantra by professors teaching Microbiology 201 “we only know of 1% of the species out there!” Also, there is a whole world of bacteria that we cannot perceive: they are too rare to come up in a microscope sample, and they are too finicky to grow on E. coli‘s favorite food, LB jello. Many are physically unreachable: they live kilometers underground, or on the ocean’s bottom, in the stratosphere, or in an insurance company’s checkbook. Many are well-hidden in plain sight: there are thousands of species in a handful of soil or a bucket of seawater: how can we possibly expect to typify them all?

The idea that there is a world of life that is hitherto unknown has always seduced us. The Kraken, Mermaids, Loch-Ness monster, Bigfoot, Yeti. We are in love with the concept of life’s rarities. Very rarely, a new mammal, reptile, bird or fish is reported. That usually goes unnoticed by the mass media, unless they are unusual, (as in butt-ugly). As a rule, we are not excited by the discovery of yet another species of fish (although we should!) but more by the “freak-appeal” of that fish. It excites us that it is strange, unusual, completely different than anything we know. It makes us happy to know that sometimes life cannot be pigeonholed. Biophilia proponents might attribute this to our inherent fascination with the diversity of life, and the role it plays in our own well-being. Remember the sealed ecosystem found in Ramla, Israel three years ago? There is the appeal of the unknown: “There’s a world going on underground”. Literally, in the Ayalon Cave. Also, the rare biosphere has an evolutionary appeal: it is the crucible of genetic novelty, where new gene variants spring eternal, and through lateral gene transfer fix themselves in the non-rare microbial communities. Unlike the isolated ecosystem of the Ayalon Cave, the rare biosphere is down under our boots, and constantly feeding the “common biosphere’s” gene pool.

New albino crustacean species from Ayalon Cave

For all these reasons, when metagenomics projects started getting off the ground, there was a lot of talk and excitement about the “rare biospehere”. Finally! Finally there is a tool with which we can gather those rare microbes and study them, at least on a genomic level. We will find the bacterial albino scorpions, an archaeal Coelacanth, and maybe even a viral Sasquatch or two. We don’t have to culture them (although we’d like to), we just need enough DNA and good computational tools to help us discover the weird genes of microbial life. And we will play Tom Waits on our MP3 players while we work at it.

Initial results were amazing: there is a world going on underground. And in the ocean, an acid mine drainage, in our guts, and on our skin. Using sequences of 16S rRNA, the “barcode of bacterial life”, to estimate the number of microbial species in a sample, a slew of new species was found. Ocean samples yielded thousands of proposed new species.

However, A recent study by Quince and colleagues published in Nature Methods tells us it may be time for a reality check. The problem being that even few reads may contain multiple errors, each one leading to unique sequences, interpreted to be new species from the rare biosphere. To correct these errors, Quince and colleagues look at the flowgram: the light intensities generated by the sequencing reaction. They used their own resequenced dataset to build an error model and better assess the diversity. Their results show that sequencing errors lead to species richness estimates that are two orders of magnitude too high.

What does this mean for the rare biosphere? It is probably out there, but the distribution tail could be much shorter than we think. Another thing is: how much influence would rare species have on the combined genomes of a microbial community or ecosystem? We don’t even know that yet. The best studies we have so far in that respect are of lateral gene transfer of antibiotic resistance, and fixation of new viral strains, especially influenza. But even here, we don’t know yet how rare is “rare”.

There’s a world going on underground. We are just beginning to bumble through it though.